Abstract:Reinforcement learning (RL) has achieved strong results in improving large language models (LLMs) on tasks with stationary, verifiable rewards, such as mathematical reasoning and code execution. In these settings, the environment follows fixed rules and does not adapt strategically to the agent. Strategic dialogue differs in this respect: the environment is another agent that adapts to the policy, and success depends on the interaction between the two sides. Despite this interactive nature, current RL approaches typically train a target agent against a fixed counterpart or simulator. We find that this training paradigm encourages the policy to exploit counterpart-specific regularities rather than learn strategies that generalize across counterparts. We call this problem the static-counterpart mismatch, which we quantify directly in our experiments. To address it, we propose Isolated Bilateral Reinforcement Learning (IB-RL), in which the two roles coevolve through joint rollouts while each role optimizes its own reward through fully independent advantages, action masks, and update paths. We evaluate frozen policies against fully independent held-out counterparts in both domains. On Vehicle TeleSales, IB-RL achieves 89.6% Success@1, compared to 84.6% for the best unilateral RL baseline. On Deal-or-NoDeal, it reaches 98.4% agreement against DeepSeek V4 Pro, compared to 86.4% for the best unilateral baseline. These results indicate that jointly training both roles with strict peragent isolation produces policies that generalize more effectively to unseen counterparts.
Abstract:Bacteriophages, often referred to as the dark matter of the biosphere, play a critical role in regulating microbial ecosystems and in antibiotic alternatives. Thus, accurate interpretation of their genomes holds significant scientific and practical value. While general-purpose Large Language Models (LLMs) excel at understanding biological texts, their ability to directly interpret raw nucleotide sequences and perform biological reasoning remains underexplored. To address this, we introduce PhageBench, the first benchmark designed to evaluate phage genome understanding by mirroring the workflow of bioinformatics experts. The dataset contains 5,600 high-quality samples covering five core tasks across three stages: Screening, Quality Control, and Phenotype Annotation. Our evaluation of eight LLMs reveals that general-purpose reasoning models significantly outperform random baselines in phage contig identification and host prediction, demonstrating promising potential for genomic understanding. However, they exhibit significant limitations in complex reasoning tasks involving long-range dependencies and fine-grained functional localization. These findings highlight the necessity of developing next-generation models with enhanced reasoning capabilities for biological sequences.